second pass base recalibration gatk4

SebBatSebBat BuffaloMember

hi there

I'm trying to run the second pass for the BaseRecalibrator with GATK4.
as seen in this post (https://gatkforums.broadinstitute.org/gatk/discussion/12985/how-to-do-a-second-pass-to-analyze-after-recalibration-in-gatk4) the previous -BQSR was substituted with -bqsr. also, it seems that there is no second pass available to do that?!

when I use it in:
GATK/gatk-4.0.12.0/gatk BaseRecalibrator \
-R CanFam3.1.dna.toplevel.fa \
-I sorted_WES_.bam \
--known-sites GATK/final.Axelsson.SNPs_nochr.vcf \
-bqsr recal.table \
-O post_recal.table

I get indeed the error "b is not a recognized option", suggesting that the option is not there..

however, the documentation here (https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.4/org_broadinstitute_hellbender_tools_walkers_bqsr_AnalyzeCovariates.php) still says that you can run it.

in the --help there is no mention of the second pass and I'm confused about what I can/should do.

also, in previous versions I used PrintReads with the recalibration table, while the first link above mentions ApplyBQSR...so, which one is the one to use?

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